SPOILER heavy.
Bingo, I think you are over thinking things way too much, and getting your timeline way mixed up.
Everything makes sense to me. The Amy and Rory we saw at the shop were an Amy and Rory from sometime down the road after the Doctor dropped them off in the last episode, meaning this episode takes place sometime after that in their timeline. If I am understanding what you are saying right, your confusion seems to be that you are under the assumption that this episode takes place in Amy and Rory's timeline prior to the Doctor's telling them to go to America. At the point we see them in this last episode, Amy already learned the word Petrichor in The Doctor's Wife.
I think it is pretty simple, the Doctor barrows the blue envelopes, dons the cowboy hat, hops in the TARDIS, and goes back in time to before this season took place and invites everyone to meet him in the States. I am sure there are some big twists coming, but I think your timeline is confused.
Bingowings said:
It's set round the time Rory and Amy get their letters that send them to America to the Doctor's date with destiny.
I think all your confusion stems from this assumption. Obviously this isn't the case, all evidence indicates otherwise.
In the photographs on the little girl's dressing table we see Amy and Baby Melody happy, this is not consistent with Amy waking up on Demon's Run with Kovarian about to steal her baby after a pregnancy she was brainwashed not to notice.
I have no idea what you are talking about right now. What episode was this? Towards the beginning of the season?